I have a maven project generated by Spring Roo and use several tools (checkstyle, pmd etc.) to collect information about my project. (namely I am using codehaus\' sonar for this
Both FindBugs and Cobertura do NOT work on the source level, but on the bytecode level. So, you should wave in your aspects statically (that would also improve application start time) at the compile time (e.g. using maven's AspectJ plugin) and not at the load time and then run static analysis tools on the result bytecode.